Impact of Bile Acid Amidation on In Silico Farnesoid X Receptor Dynamics

While the behavior of amidated bile acids has been well studied in vitro, and there is a growing body of in silico research on bile acids, the effects of amidated bile acids on the dynamics and behavior of the farnesoid X receptor (FXR) are yet to be characterized. Although amidated bile acids are larger and more hydrophobic than nonamidated bile acids, their in vitro functions can often be remarkably similar. To investigate the impact of these changes on protein behavior, classical molecular dynamics simulations were performed on the ligand-binding domain of FXR bound to the primary human bile acids and their glycine- and taurine-conjugated amidates. We observe that amino acid conjugation leads to changes in critical local interactions, including salt bridges in the binding pocket and contacts at the FXR aromatic triad. Despite these effects, the global dynamic behavior of the receptor remains surprisingly consistent across all of the ligands studied. The absence of large perturbations in FXR dynamics appears to be consistent with the reports of similar in vitro activity of glyco- and tauroconjugates with primary bile acids. Moreover, these results suggest that global versus local differences in FXR dynamics may correlate differently with experimental measurements.